BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search
Home Forums Wiki NMR feeds Downloads Register Today's Posts



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
 
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Old 12-21-2016, 07:20 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,777
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default Automated Fragmentation Polarizable Embedding DFT Calculations of NMR Shielding Constants of Proteins with Application to Chemical Shift Predictions.

Automated Fragmentation Polarizable Embedding DFT Calculations of NMR Shielding Constants of Proteins with Application to Chemical Shift Predictions.

Related Articles Automated Fragmentation Polarizable Embedding DFT Calculations of NMR Shielding Constants of Proteins with Application to Chemical Shift Predictions.

J Chem Theory Comput. 2016 Dec 19;

Authors: Steinmann C, Bratholm LA, Olsen JM, Kongsted J

Abstract
Full-protein NMR shielding constants based on ab initio calculations are desirable since they can assist in elucidating protein structures from NMR experiments. In this work we present NMR shielding constants computed using a new automated fragmentation (J. Phys. Chem. B 2009, 113, 10380--10388) approach in the framework of polarizable embedding density functional theory. We extend our previous work to give both basis set recommendations and comment on how large the quantum mechanical region should be in order to successfully compute (13)C NMR shielding constants that are comparable with experiment. The introduction of a probabilistic linear regression model allows us to substantially reduce the number of snapshots that are needed to make comparisons with experiment. This approach is further improved by augmenting snapshot selection with chemical shift predictions by which we can obtain a representative subset of snapshots that gives the smallest predicted error compared to experiment. Finally, we use this subset of snapshots to calculate the NMR shielding constants at the PE-KT3/pcSseg-2 level of theory for all atoms in the protein GB3.


PMID: 27992211 [PubMed - as supplied by publisher]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.
AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules. Related Articles AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules. J Biomol NMR. 2015 Aug 2; Authors: Swails J, Zhu T, He X, Case DA Abstract We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects...
nmrlearner Journal club 0 08-04-2015 03:00 PM
AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules
AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules Abstract We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects implicitly through a set of surface charges computed using the Poissonâ??Boltzmann equation, and it can also be combined with an explicit solvent model through the placement of water molecules in the first solvation...
nmrlearner Journal club 0 08-02-2015 07:10 AM
[NMR paper] Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.
Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method. Related Articles Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method. Adv Exp Med Biol. 2015;827:49-70 Authors: Zhu T, Zhang JZ, He X Abstract The performance of quantum mechanical methods on the calculation of protein NMR chemical shifts is reviewed based on the recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. By using the...
nmrlearner Journal club 0 11-14-2014 08:33 AM
[NMR paper] An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction.
An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction. Related Articles An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction. J Biomol NMR. 2014 Jun 19; Authors: Wiedemann C, Bellstedt P, Herbst C, Görlach M, Ramachandran R Abstract A procedure for the simultaneous acquisition of {HNCOCANH & HCCCONH} chemical shift correlation spectra employing sequential data acquisition for moderately sized...
nmrlearner Journal club 0 06-20-2014 08:14 PM
An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction
An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction Abstract A procedure for the simultaneous acquisition of {HNCOCANH & HCCCONH} chemical shift correlation spectra employing sequential \(^{1}\hbox {H}\) data acquisition for moderately sized proteins is presented. The suitability of the approach for obtaining sequential resonance assignments, including complete ...
nmrlearner Journal club 0 06-19-2014 10:21 PM
[NMR paper] Ab initio NMR chemical-shift calculations based on the combined fragmentation method.
Ab initio NMR chemical-shift calculations based on the combined fragmentation method. Related Articles Ab initio NMR chemical-shift calculations based on the combined fragmentation method. Phys Chem Chem Phys. 2013 Apr 12; Authors: Tan HJ, Bettens RP Abstract NMR chemical shift is a molecular property that can be computed from first principles. In this work we show that by utilizing our combined fragmentation method (CFM), one is able to accurately compute this property for small proteins. Without nonbonded interactions, the root mean...
nmrlearner Journal club 0 04-16-2013 07:46 PM
An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database
An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database Abstract Biomolecular NMR chemical shift data are key information for the functional analysis of biomolecules and the development of new techniques for NMR studies utilizing chemical shift statistical information. Structural genomics projects are major contributors to the accumulation of protein chemical shift information. The management of the large...
nmrlearner Journal club 0 06-16-2012 06:01 AM
[Question from NMRWiki Q&A forum] How to plot chemical shift predictions obtained form SPARTA?
How to plot chemical shift predictions obtained form SPARTA? Dear friends, I had a mutation in my protein and now I have some amino acids around mutation remained unassigned. To get a way to find the missing peaks I modelled the mutated protein with modeller and out of the pdb file I got the chemical shift predictions using SPARTA. Now that I have chemical shift predictions I want to plot them like a spectra and overlay them to my real spectra to see if it will help me to assign some of the missing peaks. I know for solid-state NMR there is a software, but what about solution NMR? ...
nmrlearner News from other NMR forums 0 11-18-2010 06:16 PM



Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is On
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 10:28 AM.


Map